Targeted protein degradation via intramolecular bivalent glues.


Journal

Nature
ISSN: 1476-4687
Titre abrégé: Nature
Pays: England
ID NLM: 0410462

Informations de publication

Date de publication:
Mar 2024
Historique:
received: 18 02 2023
accepted: 18 01 2024
medline: 8 3 2024
pubmed: 22 2 2024
entrez: 21 2 2024
Statut: ppublish

Résumé

Targeted protein degradation is a pharmacological modality that is based on the induced proximity of an E3 ubiquitin ligase and a target protein to promote target ubiquitination and proteasomal degradation. This has been achieved either via proteolysis-targeting chimeras (PROTACs)-bifunctional compounds composed of two separate moieties that individually bind the target and E3 ligase, or via molecular glues that monovalently bind either the ligase or the target

Identifiants

pubmed: 38383787
doi: 10.1038/s41586-024-07089-6
pii: 10.1038/s41586-024-07089-6
pmc: PMC10917667
doi:

Substances chimiques

Bromodomain Containing Proteins 0
Cell Cycle Proteins 0
Proteasome Endopeptidase Complex EC 3.4.25.1
Proteolysis Targeting Chimera 0
Transcription Factors 0
Ubiquitin-Protein Ligases EC 2.3.2.27

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

204-211

Subventions

Organisme : Wellcome Trust
Pays : United Kingdom

Informations de copyright

© 2024. The Author(s).

Références

Bekes, M., Langley, D. R. & Crews, C. M. PROTAC targeted protein degraders: the past is prologue. Nat. Rev. Drug Discovery 21, 181–200 (2022).
pubmed: 35042991 doi: 10.1038/s41573-021-00371-6
Hanan, E. J. et al. Monomeric targeted protein degraders. J. Med. Chem. 63, 11330–11361 (2020).
pubmed: 32352776 doi: 10.1021/acs.jmedchem.0c00093
Cowan, A. D. & Ciulli, A. Driving E3 ligase substrate specificity for targeted protein degradation: lessons from nature and the laboratory. Annu. Rev. Biochem. 91, 295–319 (2022).
pubmed: 35320687 doi: 10.1146/annurev-biochem-032620-104421
Hanzl, A. & Winter, G. E. Targeted protein degradation: current and future challenges. Curr. Opin. Chem. Biol. 56, 35–41 (2020).
pubmed: 31901786 pmcid: 7615046 doi: 10.1016/j.cbpa.2019.11.012
Han, T. et al. Anticancer sulfonamides target splicing by inducing RBM39 degradation via recruitment to DCAF15. Science 356, eaal3755 (2017).
pubmed: 28302793 doi: 10.1126/science.aal3755
Uehara, T. et al. Selective degradation of splicing factor CAPERα by anticancer sulfonamides. Nat. Chem. Biol. 13, 675–680 (2017).
pubmed: 28437394 doi: 10.1038/nchembio.2363
Bussiere, D. E. et al. Structural basis of indisulam-mediated RBM39 recruitment to DCAF15 E3 ligase complex. Nat. Chem. Biol. 16, 15–23 (2020).
pubmed: 31819272 doi: 10.1038/s41589-019-0411-6
Du, X. et al. Structural basis and kinetic pathway of RBM39 recruitment to DCAF15 by a sulfonamide molecular glue E7820. Structure 27, 1625–1633.e1623 (2019).
pubmed: 31693911 doi: 10.1016/j.str.2019.10.005
Faust, T. B. et al. Structural complementarity facilitates E7820-mediated degradation of RBM39 by DCAF15. Nat. Chem. Biol. 16, 7–14 (2020).
pubmed: 31686031 doi: 10.1038/s41589-019-0378-3
Zoppi, V. et al. Iterative design and optimization of initially inactive proteolysis targeting chimeras (PROTACs) identify VZ185 as a potent, fast, and selective von Hippel-Lindau (VHL) based dual degrader probe of BRD9 and BRD7. J. Med. Chem. 62, 699–726 (2019).
pubmed: 30540463 doi: 10.1021/acs.jmedchem.8b01413
Coomar, S. & Gillingham, D. G. Exploring DCAF15 for reprogrammable targeted protein degradation. Preprint at bioRxiv https://doi.org/10.1101/542506 (2019).
Li, L. et al. In vivo target protein degradation induced by PROTACs based on E3 ligase DCAF15. Signal Transduct. Target. Ther. 5, 129 (2020).
pubmed: 32713946 pmcid: 7383041 doi: 10.1038/s41392-020-00245-0
Ohba, K. et al. Sulfonamide or sulfinamide compound having effect of inducing BRD4 protein degradation and pharmaceutical use thereof. WIPO https://patentscope.wipo.int/search/en/detail.jsf?docId=WO2021157684 (2021).
Dai, X. et al. Prostate cancer-associated SPOP mutations confer resistance to BET inhibitors through stabilization of BRD4. Nat. Med. 23, 1063–1071 (2017).
pubmed: 28805820 pmcid: 5625299 doi: 10.1038/nm.4378
Zhang, P. et al. Intrinsic BET inhibitor resistance in SPOP-mutated prostate cancer is mediated by BET protein stabilization and AKT–mTORC1 activation. Nat. Med. 23, 1055–1062 (2017).
pubmed: 28805822 pmcid: 5653288 doi: 10.1038/nm.4379
Zengerle, M., Chan, K. H. & Ciulli, A. Selective small molecule induced degradation of the BET bromodomain protein BRD4. ACS Chem. Biol. 10, 1770–1777 (2015).
pubmed: 26035625 pmcid: 4548256 doi: 10.1021/acschembio.5b00216
Blake, R. A. et al. Preparation of tert-butyl(S)−2-(4-(phenyl)−6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]-diazepin-6-yl)acetate derivatives and related compounds as bromodomain BRD4 inhibitors for the treatment of cancer. WIPO https://patentscope.wipo.int/search/en/detail.jsf?docId=WO2020055976 (2020).
Dragovich, P., Thomas, P., Blake, R. A. & Wertz, I. Chemical inducers of degradation and methods of use. WIPO https://patentscope.wipo.int/search/en/detail.jsf?docId=WO2020086858 (2019).
Shergalis, A. G. et al. CRISPR screen reveals BRD2/4 molecular glue-like degrader via recruitment of DCAF16. ACS Chem. Biol. 18, 331–339 (2023).
pubmed: 36656921 doi: 10.1021/acschembio.2c00747
Li, Y. D. et al. Template-assisted covalent modification of DCAF16 underlies activity of BRD4 molecular glue degraders. Preprint at bioRxiv https://doi.org/10.1101/2023.02.14.528208 (2023).
Lu, G. et al. UBE2G1 governs the destruction of cereblon neomorphic substrates. eLife 7, e40958 (2018).
pubmed: 30234487 pmcid: 6185104 doi: 10.7554/eLife.40958
Mayor-Ruiz, C. et al. Plasticity of the cullin–RING ligase repertoire shapes sensitivity to ligand-induced protein degradation. Mol. Cell 75, 849–858.e848 (2019).
pubmed: 31442425 doi: 10.1016/j.molcel.2019.07.013
Chodera, J. D. & Mobley, D. L. Entropy–enthalpy compensation: role and ramifications in biomolecular ligand recognition and design. Annu. Rev. Biophys. 42, 121–142 (2013).
pubmed: 23654303 pmcid: 4124006 doi: 10.1146/annurev-biophys-083012-130318
Winter, G. E. et al. BET bromodomain proteins function as master transcription elongation factors independent of CDK9 recruitment. Mol. Cell 67, 5–18.e19 (2017).
pubmed: 28673542 pmcid: 5663500 doi: 10.1016/j.molcel.2017.06.004
Bond, A. G. et al. Development of BromoTag: a “bump-and-hole”-PROTAC system to induce potent, rapid, and selective degradation of tagged target proteins. J. Med. Chem. 64, 15477–15502 (2021).
pubmed: 34652918 pmcid: 8558867 doi: 10.1021/acs.jmedchem.1c01532
Wu, Y. et al. The DDB1–DCAF1–Vpr–UNG2 crystal structure reveals how HIV-1 Vpr steers human UNG2 toward destruction. Nat. Struct. Mol. Biol. 23, 933–940 (2016).
pubmed: 27571178 pmcid: 5385928 doi: 10.1038/nsmb.3284
Petzold, G., Fischer, E. S. & Thoma, N. H. Structural basis of lenalidomide-induced CK1α degradation by the CRL4(CRBN) ubiquitin ligase. Nature 532, 127–130 (2016).
pubmed: 26909574 doi: 10.1038/nature16979
Fish, P. V. et al. Identification of a chemical probe for bromo and extra C-terminal bromodomain inhibition through optimization of a fragment-derived hit. J. Med. Chem. 55, 9831–9837 (2012).
pubmed: 23095041 pmcid: 3506127 doi: 10.1021/jm3010515
Zhang, M. et al. Structure-based discovery and optimization of benzo[d]isoxazole derivatives as potent and selective BET inhibitors for potential treatment of castration-resistant prostate cancer (CRPC). J. Med. Chem. 61, 3037–3058 (2018).
pubmed: 29566488 doi: 10.1021/acs.jmedchem.8b00103
Zaware, N. & Zhou, M. M. Bromodomain biology and drug discovery. Nat. Struct. Mol. Biol. 26, 870–879 (2019).
pubmed: 31582847 pmcid: 6984398 doi: 10.1038/s41594-019-0309-8
Tanaka, M. et al. Design and characterization of bivalent BET inhibitors. Nat. Chem. Biol. 12, 1089–1096 (2016).
pubmed: 27775715 pmcid: 5117811 doi: 10.1038/nchembio.2209
Ren, C. et al. Spatially constrained tandem bromodomain inhibition bolsters sustained repression of BRD4 transcriptional activity for TNBC cell growth. Proc. Natl Acad. Sci. USA 115, 7949–7954 (2018).
pubmed: 30012592 pmcid: 6077712 doi: 10.1073/pnas.1720000115
Waring, M. J. et al. Potent and selective bivalent inhibitors of BET bromodomains. Nat. Chem. Biol. 12, 1097–1104 (2016).
pubmed: 27775716 doi: 10.1038/nchembio.2210
Bailey, S. & Leriche, G. Compounds and pharmaceutical compositions that modulate BRD4. WIPO https://patentscope.wipo.int/search/en/detail.jsf?docId=WO2022221786 (2022).
Tan, X. et al. Mechanism of auxin perception by the TIR1 ubiquitin ligase. Nature 446, 640–645 (2007).
pubmed: 17410169 doi: 10.1038/nature05731
Ito, T. et al. Identification of a primary target of thalidomide teratogenicity. Science 327, 1345–1350 (2010).
pubmed: 20223979 doi: 10.1126/science.1177319
Kronke, J. et al. Lenalidomide causes selective degradation of IKZF1 and IKZF3 in multiple myeloma cells. Science 343, 301–305 (2014).
pubmed: 24292625 doi: 10.1126/science.1244851
Kronke, J. et al. Lenalidomide induces ubiquitination and degradation of CK1a in del(5q) MDS. Nature 523, 183–188 (2015).
pubmed: 26131937 pmcid: 4853910 doi: 10.1038/nature14610
Sievers, Q. L. et al. Defining the human C2H2 zinc finger degrome targeted by thalidomide analogs through CRBN. Science 362, eaat0572 (2018).
pubmed: 30385546 pmcid: 6326779 doi: 10.1126/science.aat0572
Slabicki, M. et al. The CDK inhibitor CR8 acts as a molecular glue degrader that depletes cyclin K. Nature 585, 293–297 (2020).
pubmed: 32494016 pmcid: 7486275 doi: 10.1038/s41586-020-2374-x
Slabicki, M. et al. Small-molecule-induced polymerization triggers degradation of BCL6. Nature 588, 164–168 (2020).
pubmed: 33208943 pmcid: 7816212 doi: 10.1038/s41586-020-2925-1
Weng, G. et al. PROTAC-DB 2.0: an updated database of PROTACs. Nucleic Acids Res. 51, D1367–D1372 (2023).
pubmed: 36300631 doi: 10.1093/nar/gkac946
Vogel, C., Bashton, M., Kerrison, N. D., Chothia, C. & Teichmann, S. A. Structure, function and evolution of multidomain proteins. Curr. Opin. Struct. Biol. 14, 208–216 (2004).
pubmed: 15093836 doi: 10.1016/j.sbi.2004.03.011
Zhou, X., Hu, J., Zhang, C., Zhang, G. & Zhang, Y. Assembling multidomain protein structures through analogous global structural alignments. Proc. Natl Acad. Sci. USA 116, 15930–15938 (2019).
pubmed: 31341084 pmcid: 6689945 doi: 10.1073/pnas.1905068116
Cao, S. et al. Defining molecular glues with a dual-nanobody cannabidiol sensor. Nat. Commun. 13, 815 (2022).
pubmed: 35145136 pmcid: 8831599 doi: 10.1038/s41467-022-28507-1
Rui, H., Ashton, K. S., Min, J., Wang, C. & Potts, P. R. Protein–protein interfaces in molecular glue-induced ternary complexes: classification, characterization, and prediction. RSC Chem. Biol. 4, 192–215 (2023).
pubmed: 36908699 pmcid: 9994104 doi: 10.1039/D2CB00207H
Zhou, X. L. et al. A comprehensive review of BET-targeting PROTACs for cancer therapy. Bioorg. Med. Chem. 73, 117033 (2022).
pubmed: 36202064 doi: 10.1016/j.bmc.2022.117033
de Almeida, M. et al. AKIRIN2 controls the nuclear import of proteasomes in vertebrates. Nature 599, 491–496 (2021).
pubmed: 34711951 doi: 10.1038/s41586-021-04035-8
Mayor-Ruiz, C. et al. Rational discovery of molecular glue degraders via scalable chemical profiling. Nat. Chem. Biol. 16, 1199–1207 (2020).
pubmed: 32747809 pmcid: 7116640 doi: 10.1038/s41589-020-0594-x
Gong, F. et al. Screen identifies bromodomain protein ZMYND8 in chromatin recognition of transcription-associated DNA damage that promotes homologous recombination. Genes Dev. 29, 197–211 (2015).
pubmed: 25593309 pmcid: 4298138 doi: 10.1101/gad.252189.114
Imaide, S. et al. Trivalent PROTACs enhance protein degradation via combined avidity and cooperativity. Nat. Chem. Biol. 17, 1157–1167 (2021).
pubmed: 34675414 pmcid: 7611906 doi: 10.1038/s41589-021-00878-4
Li, W. et al. MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens. Genome Biol. 15, 554 (2014).
pubmed: 25476604 pmcid: 4290824 doi: 10.1186/s13059-014-0554-4
Wegner, M. et al. Circular synthesized CRISPR/Cas gRNAs for functional interrogations in the coding and noncoding genome. eLife 8, e42549 (2019).
pubmed: 30838976 pmcid: 6424562 doi: 10.7554/eLife.42549
Diehl, V. et al. Minimized combinatorial CRISPR screens identify genetic interactions in autophagy. Nucleic Acids Res. 49, 5684–5704 (2021).
pubmed: 33956155 pmcid: 8191801 doi: 10.1093/nar/gkab309
Doench, J. G. et al. Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nat. Biotechnol. 34, 184–191 (2016).
pubmed: 26780180 pmcid: 4744125 doi: 10.1038/nbt.3437
Sanson, K. R. et al. Optimized libraries for CRISPR-Cas9 genetic screens with multiple modalities. Nat. Commun. 9, 5416 (2018).
pubmed: 30575746 pmcid: 6303322 doi: 10.1038/s41467-018-07901-8
Chen, B. et al. Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell 155, 1479–1491 (2013).
pubmed: 24360272 pmcid: 3918502 doi: 10.1016/j.cell.2013.12.001
Wisniewski, J. R., Zougman, A., Nagaraj, N. & Mann, M. Universal sample preparation method for proteome analysis. Nat. Methods 6, 359–362 (2009).
pubmed: 19377485 doi: 10.1038/nmeth.1322
Wang, Y. et al. Reversed-phase chromatography with multiple fraction concatenation strategy for proteome profiling of human MCF10A cells. Proteomics 11, 2019–2026 (2011).
pubmed: 21500348 pmcid: 3120047 doi: 10.1002/pmic.201000722
Gadd, M. S. et al. Structural basis of PROTAC cooperative recognition for selective protein degradation. Nat. Chem. Biol. 13, 514–521 (2017).
pubmed: 28288108 pmcid: 5392356 doi: 10.1038/nchembio.2329
Roest, S. et al. Transfection of insect cell in suspension for efficient baculovirus generation. MethodsX 3, 371–377 (2016).
pubmed: 27222826 pmcid: 4872675 doi: 10.1016/j.mex.2016.04.011
Scholz, J. & Suppmann, S. A new single-step protocol for rapid baculovirus-driven protein production in insect cells. BMC Biotechnol. 17, 83 (2017).
pubmed: 29145860 pmcid: 5689143 doi: 10.1186/s12896-017-0400-3
Van Molle, I. et al. Dissecting fragment-based lead discovery at the von Hippel-Lindau protein:hypoxia inducible factor 1alpha protein–protein interface. Chem. Biol. 19, 1300–1312 (2012).
pubmed: 23102223 pmcid: 3551621 doi: 10.1016/j.chembiol.2012.08.015
Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017).
pubmed: 28165473 doi: 10.1038/nmeth.4169
Filippakopoulos, P. et al. Selective inhibition of BET bromodomains. Nature 468, 1067–1073 (2010).
pubmed: 20871596 pmcid: 3010259 doi: 10.1038/nature09504
Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004).
pubmed: 15572765 doi: 10.1107/S0907444904019158
Le-Trilling, V. T. K. et al. Structural mechanism of CRL4-instructed STAT2 degradation via a novel cytomegaloviral DCAF receptor. EMBO J. 42, e112351 (2023).
pubmed: 36762436 pmcid: 9975947 doi: 10.15252/embj.2022112351
Moriarty, N. W., Grosse-Kunstleve, R. W. & Adams, P. D. Electronic ligand builder and optimization workbench (eLBOW): a tool for ligand coordinate and restraint generation. Acta Crystallogr. D 65, 1074–1080 (2009).
pubmed: 19770504 pmcid: 2748967 doi: 10.1107/S0907444909029436
Mirdita, M. et al. ColabFold: making protein folding accessible to all. Nat. Methods 19, 679–682 (2022).
pubmed: 35637307 pmcid: 9184281 doi: 10.1038/s41592-022-01488-1
Evans, R. et al. Protein complex prediction with AlphaFold-Multimer. Preprint at bioRxiv, https://doi.org/10.1101/2021.10.04.463034 (2022).
Jamali, K. et al. Automated model building and protein identification in cryo-EM maps. Preprint at bioRxiv https://doi.org/10.1101/2023.05.16.541002 (2023).
Croll, T. I. ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps. Acta Crystallogr. D 74, 519–530 (2018).
doi: 10.1107/S2059798318002425
Afonine, P. V. et al. Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Crystallogr. D 74, 531–544 (2018).
doi: 10.1107/S2059798318006551
Liebschner, D. et al. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Crystallogr. D 75, 861–877 (2019).
doi: 10.1107/S2059798319011471
Pettersen, E. F. et al. UCSF ChimeraX: structure visualization for researchers, educators, and developers. Protein Sci. 30, 70–82 (2021).
pubmed: 32881101 doi: 10.1002/pro.3943
The PyMOL Molecular Graphics System, version 1.8 (Schrodinger, 2015).
Perez-Riverol, Y. et al. The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences. Nucleic Acids Res. 50, D543–D552 (2022).
pubmed: 34723319 doi: 10.1093/nar/gkab1038
Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).
pubmed: 34265844 pmcid: 8371605 doi: 10.1038/s41586-021-03819-2

Auteurs

Oliver Hsia (O)

Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK.

Matthias Hinterndorfer (M)

CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.

Angus D Cowan (AD)

Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK.

Kentaro Iso (K)

Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK.
Tsukuba Research Laboratory, Eisai Co., Ibaraki, Japan.

Tasuku Ishida (T)

Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK.
Tsukuba Research Laboratory, Eisai Co., Ibaraki, Japan.

Ramasubramanian Sundaramoorthy (R)

Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK.

Mark A Nakasone (MA)

Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK.

Hana Imrichova (H)

CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.

Caroline Schätz (C)

CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.

Andrea Rukavina (A)

CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.

Koraljka Husnjak (K)

Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany.

Martin Wegner (M)

Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany.

Alejandro Correa-Sáez (A)

Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK.

Conner Craigon (C)

Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK.

Ryan Casement (R)

Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK.

Chiara Maniaci (C)

Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK.
Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK.

Andrea Testa (A)

Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK.
Amphista Therapeutics, Cambridge, UK.

Manuel Kaulich (M)

Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany.

Ivan Dikic (I)

Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany.

Georg E Winter (GE)

CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria. gwinter@cemm.oeaw.ac.at.

Alessio Ciulli (A)

Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK. a.ciulli@dundee.ac.uk.

Articles similaires

Animals TOR Serine-Threonine Kinases Colorectal Neoplasms Colitis Mice
Databases, Protein Protein Domains Protein Folding Proteins Deep Learning
Alzheimer Disease Humans Regression Analysis Quantitative Structure-Activity Relationship Drug Design

Conservation of the cooling agent binding pocket within the TRPM subfamily.

Kate Huffer, Matthew C S Denley, Elisabeth V Oskoui et al.
1.00
TRPM Cation Channels Animals Binding Sites Mice Pyrimidinones

Classifications MeSH